Contacts of the helix formed by residues 53 - 65 (chain A) in PDB entry 2W8B
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41A PRO* 5.1 3.4 - - - +
42A PHE 5.4 0.7 + - - -
50A ALA* 5.5 0.7 - - - -
52A GLU* 1.3 81.9 + - - +
54A ILE* 1.3 62.0 + - - +
55A GLY* 3.6 2.4 + - - -
56A GLY* 2.8 27.0 + - - -
57A ILE* 3.1 15.9 + - - +
73A ARG* 2.9 35.4 + - - -
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A PHE* 3.4 34.8 - - + +
52A GLU* 3.3 18.4 + - + +
53A ASP* 1.3 71.6 - - - +
55A GLY* 1.3 64.2 + - - +
57A ILE* 3.1 8.5 + - + +
58A VAL* 2.9 23.5 + - + +
104A VAL* 3.8 24.4 - - + +
114A VAL* 3.9 20.4 - - + -
141A LEU* 3.4 32.8 - - + +
145A GLY* 3.8 23.8 - - - +
148A ALA* 5.2 1.3 - - + -
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Residues in contact with GLY 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 3.4 17.6 - - - +
40A VAL 4.1 6.1 - - - -
42A PHE* 3.8 30.7 - - - +
53A ASP* 3.4 3.9 + - - -
54A ILE* 1.3 77.0 - - - +
56A GLY* 1.3 57.1 + - - +
58A VAL* 4.5 0.7 - - - -
59A ALA* 2.9 28.1 + - - +
73A ARG* 3.7 8.3 - - - -
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Residues in contact with GLY 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A ASP* 2.8 26.0 + - - -
55A GLY* 1.3 75.5 - - - +
57A ILE* 1.3 55.4 - - - +
59A ALA* 3.4 5.9 + - - +
60A ALA* 2.9 32.3 + - - +
73A ARG* 3.2 10.6 - - - +
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Residues in contact with ILE 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A GLU* 3.9 22.4 - - + +
53A ASP 3.1 10.1 + - - +
54A ILE* 3.1 16.9 + - + +
56A GLY* 1.3 73.5 - - - +
58A VAL* 1.3 60.5 + - - +
60A ALA* 3.4 5.0 + - - +
61A ASP* 2.8 32.6 + - - +
142A ARG* 3.7 57.2 - - - +
145A GLY* 4.0 13.5 - - - -
146A HIS* 3.6 35.4 - - + +
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Residues in contact with VAL 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.9 17.9 - - + -
42A PHE* 4.5 8.1 - - + -
54A ILE* 2.9 25.2 + - + +
55A GLY 4.0 3.4 - - - +
57A ILE* 1.3 76.2 - - - +
59A ALA* 1.3 64.6 + - - +
61A ASP* 3.6 0.9 - - - +
62A LEU* 3.0 41.2 + - + +
100A VAL* 4.3 14.4 - - + -
145A GLY 3.7 12.6 - - - +
148A ALA* 4.1 11.2 - - + -
149A SER* 3.3 30.1 - - - +
152A VAL* 5.2 3.6 - - + -
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Residues in contact with ALA 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.0 18.4 - - + +
55A GLY 2.9 18.0 + - - +
56A GLY* 3.7 5.8 - - - +
58A VAL* 1.3 77.6 - - - +
60A ALA* 1.3 63.4 + - - +
62A LEU* 3.4 0.6 + - - -
63A ARG* 3.0 30.7 + - - +
70A PRO* 3.4 28.0 - - + +
73A ARG* 6.1 0.4 - - - +
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Residues in contact with ALA 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLY 2.9 21.8 + - - +
57A ILE* 3.8 6.1 - - - +
59A ALA* 1.3 72.1 - - - +
61A ASP* 1.3 60.6 + - - +
63A ARG* 3.1 19.7 + - - +
64A ASN* 2.7 43.4 + - - +
142A ARG* 6.2 1.3 - - - +
188A ASP* 6.2 0.2 - - - +
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Residues in contact with ASP 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ILE* 2.8 21.2 + - - +
58A VAL 3.6 0.2 - - - +
60A ALA* 1.3 74.6 - - - +
62A LEU* 1.3 63.4 + - - +
64A ASN* 3.0 11.3 + - - +
65A SER 3.1 3.8 + - - -
146A HIS* 2.7 39.8 + - - -
149A SER* 2.6 34.0 + - - +
163A PHE* 3.0 33.1 - - + +
187A TYR* 2.7 28.3 + - - -
188A ASP* 4.2 3.1 - - - +
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Residues in contact with LEU 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ILE* 3.6 36.1 - - + -
39A VAL* 4.4 4.7 - - + -
58A VAL* 3.0 30.1 + - + +
59A ALA 3.9 2.9 - - - +
61A ASP* 1.3 79.0 - - - +
63A ARG* 1.3 61.0 + - - +
65A SER* 2.6 24.0 + - - -
68A PHE* 3.5 36.9 + - + +
70A PRO* 4.6 3.8 - - + -
149A SER* 4.2 10.5 - - - +
152A VAL* 4.1 11.4 - - + -
153A PHE* 4.0 31.9 - - + +
163A PHE* 4.2 5.2 - - + -
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Residues in contact with ARG 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A ILE* 3.8 24.0 - - + +
30A GLY 4.8 11.3 - - - +
31A VAL* 6.3 1.6 - - - +
32A ASP 6.2 1.6 - - - +
59A ALA* 3.0 20.9 + - - +
60A ALA* 3.6 23.5 - - - +
62A LEU* 1.3 75.4 - - - +
64A ASN* 1.3 62.8 + - - +
65A SER 3.0 2.3 + - - -
66A GLY* 3.0 12.8 + - - -
68A PHE 3.6 16.1 - - - +
69A ASN* 5.5 2.5 + - - +
70A PRO* 3.9 36.4 + - + +
71A LEU 5.7 0.8 + - - -
72A ASP* 6.0 4.2 - - - +
410A PHE* 3.7 9.0 - - - -
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ILE* 3.5 34.8 - - + +
27A ILE* 3.7 17.7 - - - +
60A ALA* 2.7 30.5 + - - +
61A ASP* 3.0 8.2 + - - +
63A ARG* 1.3 72.4 - - - +
65A SER* 1.3 62.1 + - - +
66A GLY 3.1 1.0 + - - -
187A TYR* 3.0 29.6 + - + +
188A ASP* 4.5 5.5 - - - +
388A MET* 3.5 14.9 - - - +
410A PHE* 3.5 17.6 - - + -
1431A SO4 3.5 9.9 + - - +
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Residues in contact with SER 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ASP 3.1 9.6 + - - -
62A LEU 2.6 21.1 + - - -
63A ARG 3.0 0.6 - - - -
64A ASN* 1.3 78.9 - - - +
66A GLY* 1.3 56.6 + - - +
67A LYS* 3.0 31.2 + - - +
68A PHE* 3.8 1.4 - - - -
153A PHE* 3.6 29.0 - - - -
163A PHE* 3.9 8.7 - - - -
387A THR* 5.1 4.1 + - - +
388A MET* 3.4 14.8 - - - +
405A SER* 5.2 2.3 - - - -
410A PHE* 5.1 0.2 - - - +
1431A SO4 3.5 13.2 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il